High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

Abstract

Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1-V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

“…1A, Table 1). DMSP lyase enzymes are distributed among multiple protein 1 families, but all lead to the production of DMS and either acrylate (DddL,P,Q,W,Y) or 3-2 hydroxypropionate (3-HP; DddD) 9 . The HTCC1062 genome encodes annotated genes for all 3 steps in the degradation of acrylate to propionyl-CoA or acetyl-CoA (Fig.…”

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

“…Alternatively, since no Cyanobacteria were found in our 890 m clone libraries, other bacteria with the same ITS length as cyanobacteria may inhabit the mesopelagic. The depth structure and seasonal patterning of SAR11, and their sister clade AEGEAN-169 (Supplementary Figure S4A, Supplementary Table S4) reflect patterns seen at BATS (Carlson et al, 2009, 11;Vergin et al, 2013a). The seasonality of individual OTUs within the non-seasonal SAR11 Surface 1 clade (Supplementary Tables S4, S5) suggested that this finer resolution is important in understanding the dynamics of this abundant group.…”

Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria

“…In the Sargasso Sea, total Pelagibacterales cell abundances oscillate between 0.5 and 2.2 Â 10 8 cells l À 1 with maximum abundances at or above the pycnocline 40 . Spatiotemporal variation in the distribution of Pelagibacterales ecotypes has been discussed in multiple studies 31,40,41 . The degree to which the presence of C-P lyase genes correlates with the different Pelagibacterales ecotypes and whether the relative abundances of Pelagibacterales-like C-P lyase genes fluctuate seasonally is unknown.…”