Seed Bank and Seasonal Patterns of the Eukaryotic SAR (Stramenopila, Alveolata and Rhizaria) Clade in a New England Vernal Pool

Vernal pools are dynamic freshwater ecosystems that dry during the summer. These unique habitats are vital to a number of well-studied animal species but there is little documentation of the diversity of the SAR—Stramenopila, Alveolata and Rhizaria—clade in vernal pools. Here, we characterize the protist community over a portion of the hydroperiod as the vernal pool transitions from its winter stage through its drying out in late summer. Our study focuses on the SAR clade, which encompasses a broad range of morphological diversity and a variety of trophic modes within the microbial food web. Using high-throughput sequencing, we investigate the total community (DNA) and the active (RNA) members on a temporal scale. These molecular data reveal seasonality within microbial communities, suggesting a larger community of autotrophs in the winter followed by an increase in heterotrophs in the summer. Our analysis also suggests the presence of a microbial seed bank, a collection of encysted protists, in the sediments below the pool. We hypothesize the seed bank allows for community turnover: taxa encyst in the sediment in poor environmental conditions and exit their cysts when favorable conditions occur. We also observe seasonal preference and partitioning of the environment within clades of close relatives, including taxa closely related to the ciliate Halteria and the oomycete Haptoglossa. These data provide insights into the seasonal patterns of a frequently overlooked group of organisms in this unusual environment

Insights into Transgenerational Epigenetics from Studies of Ciliates

Epigenetics, a term with many meanings, can be broadly defined as the study of dynamic states of the genome. Ciliates, a clade of unicellular eukaryotes, can teach us about the intersection of epigenetics and evolution due to the advantages of working with cultivable ciliate lineages, plus their tendency to express extreme phenotypes such as heritable doublet morphology. Moreover, ciliates provide a powerful model for studying epigenetics given the presence of dimorphic nuclei – a somatic macronucleus and germline micronucleus – within each cell. Here, we exemplify the power of studying ciliates to learn about epigenetic phenomena. We highlight “classical” examples from morphology and physiology including cortical inheritance, mating type determination, and serotype expression. In addition, we detail molecular studies of epigenetic phenomena, including: DNA elimination; alternative processing and unscrambling; and copy number determination. Based on the implications of these studies, we discuss epigenetics as a possible functional mechanism for rapid speciation in ciliates

Cannibalism in Blepharisma americanum : a genome comparison

Cannibalism is a process in which an organism consumes a member of its own species. The process is intraspecies while predation is interspecies. Unlike predation, literature on the process of cannibalism is largely understudied, particularly in the microbial world. This study focuses on Blepharisma americanum , a species of eukaryotic microbe. In this species, cannibalism can be confirmed visually by a giant cannibal cell digesting victim cells within the food vacuoles. Cannibalism is regularly practiced in B. americanum and I attempt to elucidate the genetic differences between life states: cannibal and vegetative cells. I investigate using bioinformatic approaches: whole transcriptome amplification, high throughput sequencing, and phylogenomic transcript analysis. The data show heterogeneous transcript diversity between life states, indicating that while life state is determined visually, the genetic processes behind the state may be more complex. I also identified 15 candidate cannibalism gene families that are upregulated or downregulated in cannibal cells. Of the 15 gene families, I was able to link two of them to protein families involved in the autophagosome and membrane growth. I hope that future studies can continue to use the power of molecular study and bioinformatics to further the genetic study cannibalism in B. americanu