Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms

Abstract

The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso- to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8-V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2741 (V4) and 2606 (V8-V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. About 18.4% (V4) and 13.8% (V8-V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply-branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information.

Microbial community structure in the western tropical South Pacific

“…Especially over the last 10 years, molecular methodologies have allowed for the characterization of these groups at the taxon or species level, revealing enormous diversity across all trophic levels of marine microbial communities and identifying numerous ecotypes occupying distinct ecological niches (Carlson et al, 2007;Venter et al, 2004). More recently, environmental sequencing has revealed a surprising diversity of small-sized PPE and new eukaryotic lineages continue to be discovered and characterized (Kashtan et al, 2014;Kim et al, 2016;Lepère et al, 2009;Rii et al, 2016a), while also revealing the importance of viruses in regulating phytoplankton communities (Brum et al, 2015;Huang et al, 2015).…”

Microbial community structure in the Western Tropical South Pacific

“…More recently, environmental sequencing has revealed a surprising diversity of small sized picophytoeukaryotes (PPE) and new eukaryotic lineages continue to be discovered and characterized (Kashtan et al, 2014;Kim et al, 2016;Lepère et al, 2009;Rii et al, 2016b) while also revealing the importance of viruses in regulating phytoplankton communities (Brum et al, 2015;Huang et al, 2015).…”

Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina

“…Purification was done following the manufacturer instructions. PCR amplification of either the V4 or V8-9 regions of 18S rDNA were performed as previously described (Kim et al, 2016). Both V4 and V8-9 regions of the 18S rRNA gene were sequenced because of their extensive use for eukaryotic diversity (Nickrent and Sargent, 1991;Amaral-Zettler et al, 2009;Massana et al, 2015) and to compensate the existing primer bias of each region.…”

“…Both V4 and V8-9 regions of the 18S rRNA gene were sequenced because of their extensive use for eukaryotic diversity (Nickrent and Sargent, 1991;Amaral-Zettler et al, 2009;Massana et al, 2015) and to compensate the existing primer bias of each region. Amplicon libraries were prepared as in Kim et al (2016) (further details about library preparation can be found in Supplementary Table). Sequencing was performed on Illumina MiSeq platform (2 × 300 bp) at the Cornell University Sequencing Core (New York; USA).…”

“…These clean reads were then clustered into Operational Taxonomic Units (OTUs) using UPARSE with a 97% similarity threshold, resulting in a total of 4,598 OTUs for V4 and 4,176 OTUs for V8-9 region. Even though there is no clear consensus on the optimal threshold to use in clustering algorithms Brown et al, 2015), we decided to use 97% because it has been widely used (Stoeck et al, 2010;Kammerlander et al, 2015;Massana et al, 2015;Giner et al, 2016;Kim et al, 2016). We are aware that this threshold might group species or even genus into the same OTU.…”