Biology subjects

Coots, N. L.

Publications and source records attributed to Coots, N. L..

4 recordsLinked to original sources

bioRxiv2026

Phylogenetic position and expanded host range of the photosymbiont Brandtodinium nutricula (Peridiniales, Dinophyceae)

Brandtodinium nutricula is a dinoflagellate species commonly reported in symbiosis with the marine protist host lineage, Collodaria (Rhizaria). Despite the widespread abundance of this symbiosis throughout the open ocean, and clear indications that the alga should be capable of existing outside of the symbiosis, there are no reports to date of the alga in free-living form in the environment. Even though B. nutricula molecular data are publicly available, the phylogenetic position of B. nutricula remains unclear. Our taxon-rich 18S rRNA gene phylogenetic analysis revealed a close association between B. nutricula and the copepod parasite lineage, Blastodinium. We next analyzed Tara Oceans metabarcode data to assess B. nutricula abundance outside of the Collodaria symbiosis and found that B. nutricula is common in free-living form throughout the sunlit ocean. Similarly, B. nutricula does not significantly correlate with Collodaria in terms of read depth in Tara Oceans samples, despite their tight association. We also determined that B. nutricula can live symbiotically within planktonic Foraminifera using fluorescence lifetime imaging microscopy in combination with fluorescence in situ hybridization. These findings indicate that the radiolarian-B. nutricula symbiosis is less specific than previously suggested, highlighting the complexity of open ocean symbioses and the importance of weighing both host and symbiont perspectives when considering who benefits from the relationship.

ecology↗

bioRxiv2026

Fluorescence Lifetime Imaging Microscopy (FLIM) as a method to elucidate trends in marine planktonic symbioses

The Retaria are an abundant planktonic protist lineage that play a substantial role in biogeochemical cycling, primary production, and food web dynamics in open ocean ecosystems. Their impact is, in large part, due to their capacity to host photosynthetic endosymbionts. Despite the importance of these relationships in the global oceans, our knowledge about the diversity of photosymbionts associated with the planktonic Retaria is still limited due to the difficulty of collecting and analyzing these cells. Here we apply a new protocol to assess retarian photosymbiont diversity: Fluorescence Lifetime Imaging Microscopy (FLIM) is an easy-to-use method to distinguish between different sources of fluorescence during confocal microscopy. We applied FISH probes that hybridize with the most commonly reported retarian photosymbiont lineages to environmental plankton samples and used FLIM to confirm the presence or absence of our FISH probes in retarian cells. By analyzing the fluorescence lifetime of 92 photosymbionts, we found that the retarian photosymbiosis is far more complex than originally described, where Retaria commonly host multiple algal lineages per cell, and regularly host algal lineages outside of the two most common lineages. These efforts demonstrate that FLIM is an overlooked tool in the study of host-microbe associations, with significant potential to be used across diverse host lineages and environmental samples.

ecology↗

bioRxiv2023

Single-cell genomics reveals the divergent mitochondrial genomes of Retaria (Foraminifera and Radiolaria)

Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria--the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we present two complete mitochondrial genomes of Foraminifera and two near-complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes encode a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and encode only 14-15 protein-coding genes, including nad1, 3, 4, 4L, 5, 7, cob, cox1, 2, 3, atp1, 6, and 9, with forams and radiolarians additionally encoding nad2 and nad6, respectively. In radiolarian mitogenomes, a non-canonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases.

genomics↗

bioRxiv2019

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be \"hot spots\" for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.

molecular biology↗