Morphological Identification and Single-Cell Genomics of Marine Diplonemids

Published in Current Biology

Morphological Identification and Single-Cell Genomics of Marine Diplonemids

Ryan M.R. Gawryluk, Javier del Campo, Noriko Okamoto, Jürgen F.H. Strassert, Julius Lukeš, Thomas A. Richards, Alexandra Z. Worden,  Alyson E. Santoro, Patrick J. Keeling

Recent global surveys of marine biodiversity have revealed that a group of organisms known as ‘‘marine diplonemids’’ constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago, their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small sub- unit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids, isolated from a range of depths in the eastern North Pacific Ocean. Phylogenetic analysis confirms that the isolates reflect the entire range of marine diplonemid diversity, and comparisons to environmental SSU surveys show that sequences from the isolates range from rare to superabundant, including the single most common marine diplonemid known. SCG generated a total of ~915 Mbp of assembled sequence across all ten cells and ~4,000 protein-coding genes with homologs in the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed across categories expected for heterotrophic protists. Models of highly conserved genes indicate a high density of non-canonical introns, lacking conventional GT-AG splice sites. Mapping metagenomic datasets to SCG assemblies reveals virtually no overlap, suggesting that nuclear genomic diversity is too great for representative SCG data to provide meaningful phylogenetic context to metagenomic datasets. This work provides an entry point to the future identification, isolation, and cultivation of these elusive yet ecologically important cells. The high density of nonconventional introns, however, also portends difficulty in generating accurate gene models and highlights the need for the establishment of stable cultures and transcriptomic analyses.

The ‘other’ coral symbiont: Ostreobium diversity and distribution

ostreobium

Published in The ISME Journal

The ‘other’ coral symbiont: Ostreobium diversity and distribution

Javier del Campo, Jean-François Pombert, Jan Šlapeta, Anthony Larkum, Patrick J. Keeling

Ostreobium is an endolithic algal genus thought to be an early-diverging lineage of the Bryopsidales (Ulvophyceae, Chlorophyta). Ostreobium can live in low-light conditions on calcium carbonate substrate in tropical conditions. It is best known as a symbiont of corals, where it lives deep within the animal skeleton and exchanges nitrogen and carbon, as well as providing nutrients and photoassimilates. In contrast to the relatively well-studied role of the photosynthetic zooxanthellae symbionts in coral (Symbiodinium), Ostreobium phylogeny, diversity and distribution are all poorly understood. Here, we describe the phylogenetic position and diversity of Ostreobium based on plastid 16S ribosomal DNA (rDNA), 18S rDNA and rbcL genes from a nuclear genome survey and complete plastid genome, and determined its environmental diversity and distribution by screening the publicly available environmental data for those genes. The results shed light on the phylogeny and the ecology of the ‘other’ coral symbiont.

Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes

labys

Published in The Journal of Eukaryotic Microbiology.

Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes

Jingwen Pan, Javier del Campo, Patrick J. Keeling

Labyrinthulomycetes are heterotrophic stramenopiles that are ubiquitous in a wide range of both marine and freshwater habitats and play important roles in decomposition of organic matter. The diversity and taxonomy of Labyrinthulomycetes has been studied for many years, but we nevertheless lack both a comprehensive reference database and up-to-date phylogeny including all known diversity, which hinders many global insights into their ecological distribution and the relative importance of various subgroups in different environments. Here, we present a curated reference database and a phylogenetic tree of Labyrinthulomycetes small subunit ribosomal RNA (SSU or 18S rRNA) data. Based on this created reference database, we analyzed high-throughput environmental sequencing data, revealing many previously unknown environmental clades and exploring the ecological distribution of various subgroups. Particularly, a number of newly identified environmental clades that are widespread in the open ocean. Comparing the manually curated reference database to existing tools for identification of environmental sequences (e.g. PR2 or SILVA databases) suggests that the curated database provides a higher degree of specificity and a lower frequency of misidentification. The phylogenetic framework and database will be a useful tool for future ecological and evolutionary studies.