Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays

Abstract

Marine Synechococcus diversity has been previously described using multi-locus gene sequence phylogenies and the identification of distinct clades. Synechococcus from Clades I, II, III, and IV and from sub-clades within Clades I and IV were enumerated from environmental samples by developing a hybridization assay to liquid bead-arrays (Luminex). Oligonucleotide probes targeting a gene encoding a subunit of RNA polymerase (rpoC1) were used simultaneously in multiplexed assays to track Synechococcus diversity from a Pacific Ocean coastal monitoring site and along a coastal to open-ocean transect in the Southern California Bight. The Luminex assay demonstrated that Synechococcus from Clades I and IV were the dominant types at the coastal site throughout the year. Synechococcus from Clades II and III were not detected except during the late summer or early winter. Within the dominant Clades I and IV, rpoC1-defined sub-clades of Synechococcus showed distinct spatial distributions along the coastal to open-ocean transect, coinciding with changes in the nitricline, thermocline, and fluorescence (chlorophyll) maximum depths. In coastal waters, Synechococcus targeted by 2 sub-clade IV probes were dominant at the surface, whereas 2 sub-clade I probes and a third sub-clade IV probe had increased signals in deeper water near the fluorescence maximum. In mesotrophic waters, this third sub-clade IV probe dominated at the fluorescence maximum (depth of 50 to 70 m), whereas all other sub-clade probes were below detection limits. The differing distributions of sub-clades within the dominant Synechococcus clades indicate that the subclades likely have adapted to distinct ecological niches found within the Southern California Bight. KEY WORDS: Cyanobacteria · Microbial ecology · Biogeography · Time-series · LuminexResale or republication not permitted without written consent of the publisher Mar Ecol Prog Ser 426: 133-147, 2011, Zwirglmaier et al. 2008) and off-shore oligotrophic environments (Ferris & Palenik 1998, Toledo & Palenik 2003, Ahlgren & Rocap 2006. Physiologically, differences in growth rates, in nitrogen and phosphate utilization, in pigment composition, in chromatic adaptation, and in motility have typically been used to describe isolated strains of Synechococcus (Moore et al. 1995, Collier et al. 1999, Toledo et al. 1999, Ahlgren & Rocap 2006, but, with the exception of motility (which has been found only in Clade III isolates), phenotypic traits and adaptations that uniquely characterize the genetically defined clades have yet to be identified.To understand the ecology of Synechococcus, diversity and abundance measures are fundamental. However, due to their small size, obtaining these measures is technically challenging. Traditionally, microbes are often distinguished physiologically by studying cultured isolates. But since only a small fraction of microbial diversity is represented by cultured isolates, and since the process of cultivation is labor-intensive, culture-independent and molecular methods h...

Genomic island genes in a coastal marine Synechococcus strain confer enhanced tolerance to copper and oxidative stress

“…At 60 m at site 93.40 the sharp decrease in total Synechococcus numbers (Tai et al, 2011) coincides well with a clear increase in Cu 2 þ concentration as found using CLE-ACSV ( Figure 5, Supplementary Figure S8) (Buck and Bruland 2005;Buck et al, 2010)), and the largest positive difference between total dissolved copper and free Cu 2 þ occurs at the depth (30 m) with maximal Synechococcus numbers. Accordingly, we would predict that site 93.65, which has two to four times higher abundance of Synechococcus, might have lower free copper levels due to high levels of organic ligand.…”

“…In Tai et al (2011) distribution of several subclades from clades I and IV were quantified at these sites and it was found that at site 93.40 (and other coastal stations) the main clade I groups increased with depth, whereas the dominant clade IV group decreased with depth. In contrast, at site 93.65 most of the groups increased with depth and thus, at depth these sites had quite different relative abundances of the various groups.…”

“…QPCR was performed on a Stratagene Mx300P using Promega GoTaq qPCR master mix (Promega, Madison, WI, USA) according to the manufacturer's specifications. QPCR samples included DNA from monthly samples from 2005 (no February or August samples due to sample loss) and 2007 from ) and DNA from depth samples collected in July, 2007 as described in Tai et al, 2011. QPCR primers used on above samples were for sync_1495 and rpoc Clade I (Supplementary Table S1).…”

Population dynamics and diversity of Synechococcus on the New England Shelf

“…Different subclade distributions have also been observed off the southern coast of California. Tai et al [105] found that subclades within clades I and IV showed distinct depth distributions along a coastal to open ocean transect, suggesting that these subclades are likely to have preferred environments. At MVCO, we did not, however, find correlation between the relative abundance of sequences for each subclade and nutrient concentrations or temperature (data not shown).…”

“…This conclusion is also consistent with findings in other coastal systems. Tai et al [105] found that subclades within clades I and IV showed distinct depth distributions along a coastal to open ocean transect, suggesting these subclades have preferred environments. It seems clear that not all members of a clade may respond in the same way to the environment, and further exploration of the microdiversity is needed.…”