MEPS 426:133-147 (2011)  -  DOI: https://doi.org/10.3354/meps09030

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

Vera Tai1,2, Ronald S. Burton1, Brian Palenik1,*

1Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego,
9500 Gilman Drive, La Jolla, California 92093, USA
2Present address: Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
*Corresponding author. Email:

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 sub-clades likely have adapted to distinct ecological niches found within the Southern California Bight.


KEY WORDS: Cyanobacteria · Microbial ecology · Biogeography · Time-series · Luminex


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Cite this article as: Tai V, Burton RS, Palenik B (2011) Temporal and spatial distributions of marine Synechococcus in the Southern California Bight assessed by hybridization to bead-arrays. Mar Ecol Prog Ser 426:133-147. https://doi.org/10.3354/meps09030

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