Metagenomes of the Picoalga Bathycoccus from the Chile Coastal Upwelling

Abstract

Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome.

Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses

“…Searches against genomic survey sequence, WGS and high-throughput genomic sequence libraries were performed using tBLASTn, whereas BLASTp was used to compare CHIV CP sequences to metagenomic proteins (env_nr). Putative CHIVs were detected in metagenomes targeting the small eukaryotic fraction in coastal upwelling waters off central Chile (NCBI GI:372349332 and 393314887) 37 . Reads from these two data sets were assembled with the same pipeline as the viromes, and three putative CHIV genomes were obtained.…”

Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

“…The class Mamiellophyceae (Marin and Melkonian, 2010), corresponding to clade II , contains three important genera of marine pico-phytoplankton: Micromonas, Bathycoccus and Ostreococcus. They are typical of coastal waters Romari and Vaulot, 2004;Collado-Fabri et al, 2011) where they can form sporadic blooms (O'Kelly et al, 2003) but have also been observed in open oceanic waters (Foulon et al, 2008;Monier et al, 2012;Treusch et al, 2012;Vaulot et al, 2012). The genus Micromonas can be dominant in Arctic ecosystems (Lovejoy et al, 2007;Balzano et al, 2012).…”

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean

“…However, targeted metagenomic data from the tropical Atlantic suggest that different Bathycoccus ecotypes may exist, based largely on an intron/intein presence/absence polymorphism in the gene PRP8 (18,19). Notably, the internal transcribed spacer (ITS) from the tropical Atlantic wild Bathycoccus metagenome also branches separately from cultured strains (18), while the ITS from cultured strains and two coastal Chilean Bathycoccus metagenomes are similar (20). Sequence variations have led to the proposal that two (18) or more (20) ecotypes exist and that the ecotypes may partition between mesotrophic and oligotrophic environments (18).…”

“…Notably, the internal transcribed spacer (ITS) from the tropical Atlantic wild Bathycoccus metagenome also branches separately from cultured strains (18), while the ITS from cultured strains and two coastal Chilean Bathycoccus metagenomes are similar (20). Sequence variations have led to the proposal that two (18) or more (20) ecotypes exist and that the ecotypes may partition between mesotrophic and oligotrophic environments (18). However, little is known about overall genetic distances and whether the observed sequence variants do indeed correspond to ecotype-level differences.…”