A novel clade of Prochlorococcus found in high nutrient low chlorophyll waters in the South and Equatorial Pacific Ocean

Abstract

A novel high-light (HL)-adapted Prochlorococcus clade was discovered in high nutrient and low chlorophyll (HNLC) waters in the South Pacific Ocean by phylogenetic analyses of 16S ribosomal RNA (rRNA) and 16S-23S internal transcribed spacer (ITS) sequences. This clade, named HNLC fell within the HL-adapted Prochlorococcus clade with sequences above 99% similarity to one another, and was divided into two subclades, HNLC1 and HNLC2. The distribution of the whole HNLC clade in a northwest to southeast transect in the South Pacific (HNLC-to-gyre) and two 81 N to 81 S transects in the Equatorial Pacific was determined by quantitative PCR using specific primers targeting ITS regions. HNLC was the dominant HL Prochlorococcus clade (2-9% of bacterial 16S rRNA genes) at the three westernmost stations in the South Pacific but decreased to less than 0.1% at the other stations being replaced by the eMIT9312 ecotype in the hyperoligotrophic gyre. The highest contributions of HNLC Prochlorococcus in both Equatorial Pacific transects along the latitudinal lines of 1701 W and 1551 W were observed at the southernmost stations, reaching 16 and 6% of bacterial 16S rRNA genes, respectively, whereas eMIT9312 dominated near the Equator. Spearman Rank Order correlation analysis indicated that although both the HNLC clade and eMIT9312 were correlated with temperature, they showed different correlations with regard to nutrients. HNLC only showed significant correlations to ammonium uptake and regeneration rates, whereas eMIT9312 was negatively correlated with inorganic nutrients.

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

“…In contrast, the single-cell approach described here provides unequivocal linkages among functional genes, 16S rRNA and ribosomal ITS sequences. Thus, we were able to compare our single cells with the gene sequences of the previous studies and determine if the functional genes identified by Rusch et al (2010) are associated with the 16S rRNA sequences identified by West et al (2011). Phylogenetic analyses confirm the same novel clades of Prochlorococcus were identified independently in all three cases (Figure 2).…”

“…However, it was unclear whether these previously described clades are the same as connections could not be made between the core functional genes reported by Rusch et al (2010) and the 16S rRNA sequences reported in West et al (2011). The partial genomes assembled de novo by Rusch et al (2010) from metagenomic sequences were not suitable for phylogenetic analysis because the genomes, and the genes comprising them, were composites derived from multiple organisms.…”

“…When possible, we also included 16S and rptS sequences from single cells in the corresponding trees, but sequences were not available for every cell due to incomplete genome recovery. Finally, we included the same rptS sequences used by Rusch et al (2010) and 16S rRNA sequenced used by West et al (2011) in their phylogenetic analyses of the HL III and HL IV clades.…”

“…Analyses of environmental DNA sequences have recently revealed new clades of HL-adapted Prochlorococcus that currently lack cultured representatives (Rusch et al, 2010;West et al, 2011;Huang et al, 2012). More specifically, Rusch et al (2010) identified two groups through phylogenetic analysis of several 'core' functional genes, that is, those common to all sequenced Prochlorococcus genomes, from the Global Ocean Survey (GOS) metagenomic data set, whereas West et al (2011) recovered novel 16S rRNA sequences in a separate sampling expedition.…”

“…More specifically, Rusch et al (2010) identified two groups through phylogenetic analysis of several 'core' functional genes, that is, those common to all sequenced Prochlorococcus genomes, from the Global Ocean Survey (GOS) metagenomic data set, whereas West et al (2011) recovered novel 16S rRNA sequences in a separate sampling expedition. In both cases, these new clades were abundant in high nutrient low chlorophyll (HNLC) regions of the ocean where low iron concentrations limit primary production (Martin et al, 1994).…”