Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern Ocean

Abstract

We assessed the composition of the bacterioplankton in the Atlantic sector of the Southern Ocean in austral fall and winter and in New Zealand coastal waters in summer. The various water masses between the subtropics/Agulhas-Benguela boundary region and the Antarctic coastal current exhibited distinct bacterioplankton communities with the highest richness in the polar frontal region, as shown by denaturing gradient gel electrophoresis of 16S rRNA gene fragments. The SAR11 clade and the Roseobacter clade-affiliated (RCA) cluster were quantified by real-time quantitative PCR. SAR11 was detected in all samples analysed from subtropical waters to the coastal current and to depths of > 1000 m. In fall and winter, this clade constituted < 3% to 48% and 4-28% of total bacterial 16S rRNA genes respectively, with highest fractions in subtropical to polar frontal regions. The RCA cluster was only present in New Zealand coastal surface waters not exceeding 17 degrees C, in the Agulhas-Benguela boundary region (visited only during the winter cruise), in subantarctic waters and in the Southern Ocean. In fall, this cluster constituted up to 36% of total bacterial 16S rRNA genes with highest fractions in the Antarctic coastal current and outnumbered the SAR11 clade at most stations in the polar frontal region and further south. In winter, the RCA cluster constituted lower proportions than the SAR11 clade and did not exceed 8% of total bacterial 16S rRNA genes. In fall, the RCA cluster exhibited significant positive correlations with latitude and ammonium concentrations and negative correlations with concentrations of nitrate, phosphate, and for near-surface samples also with chlorophyll a, biomass production of heterotrophic prokaryotes and glucose turnover rates. The findings show that the various water masses between the subtropics and the Antarctic coastal current harbour distinct bacterioplankton communities. They further indicate that the RCA cluster, despite the narrow sequence similarity of > 98% of its 16S rRNA gene, is an abundant component of the heterotrophic bacterioplankton in the Southern Ocean, in particular in its coldest regions.

Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects

“…This threshold has been widely used for the delineation of bacterial species, allowing our results to be compared with past and future studies that adopt this criterion. Unique OTUs (15,868) were identified across all fractions of all samples, 13,011 of which were generated de novo; that is, they did not cluster with sequences in the SILVA database. In many samples and size fractions, the total abundance of OTUs generated de novo was greater than that of OTUs identified by clustering with SILVA seed sequences (Fig.…”

“…The higher abundance of Bacteroidetes at the surface reflects their association with phytoplankton, as many species in this lineage specialize in the degradation of high molecular weight products of primary production 20 . Alphaproteobacteria were represented primarily by the SAR11 clade, abundant in ocean surface communities 21 including the SO 22 , and Roseobacter clades, which have also been associated with degradation of phytoplankton products 15,20 (Supplementary Data 2). The dominant Gammaproteobacterial orders were the Alteromonadales and Oceanospirillales, typical of SO surface waters 23 .…”

“…Hence, it would be expected that locations that are closely connected by advection would have more similar compositions than those that are not, even when the environment effect is accounted for. Indeed, advection is often invoked to explain observations of microbial diversity or abundance, which do not seem attributable to environmental selection (for example, refs [13][14][15][16]. The exchange of very small volumes of water between marine microbial mesocosms has been found to greatly reduce their b-diversity (in this case, compositional differences between communities from different mesocosms) even under consistent environmental conditions 17 .…”

Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria

“…Nucleic acid extraction DNA for subsequent screening with a PCR specific for the marine myxobacteria cluster (MMC) was extracted following the protocol of Zhou and colleagues (1996), with modifications described by Giebel et al (2009). DNA extraction was checked on a 1% agarose gel.…”

Distribution of Roseobacter RCA and SAR11 lineages in the North Sea and characteristics of an abundant RCA isolate

“…At present, it is well established that mainly Alphaproteobacteria and Gammaproteobacteria, as well as Sphingobacteria and Flavobacteria constitute (photo)heterotrophic bacterioplankton communities in near-surface marine pelagic environments (Morris et al, 2005;Fuhrman et al, 2006;AlonsoSáez et al, 2007;Malmstrom et al, 2007;West et al, 2008;Alonso-Gutiérrez et al, 2009;Giebel et al, 2009). Prominent components include the SAR11, Roseobacter and SAR86 clades and the OM60/NOR5 cluster.…”