Palenik B, Ren Q, Dupont CL, Myers GS, Heidelberg JF, Badger JH et al.. Genome sequence of Synechococcus CC9311: insights into adaptation to a coastal environment. Proc Natl Acad Sci USA 103: 13555-13559

Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 10/2006; 103(36):13555-9. DOI: 10.1073/pnas.0602963103
Source: PubMed


Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.

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Available from: Anthony Scott Durkin, Jun 25, 2014
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    • "In comparison, Synechococcus CC9311 lacks a phosphate sensor-response regulator system and an alkaline phosphatase as well as having fewer genes for periplasmic phosphate binding proteins used in the transport system (Palenik et al., 2006). These predicted differences in gene content for phosphate acquisition and regulation have been linked to the availability of phosphate in the ocean environment (Palenik et al., 2006). Although we do not determine a mechanism between genome content and growth physiology under low P concentrations , our observations are consistent with the hypothesis that WH8102 is better adapted to growth under low P conditions. "
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    ABSTRACT: Phosphate (P) is an important nutrient potentially limiting for primary productivity, yet, we currently know little about the relationship between growth rate and physiological response to P limitation in abundant marine Cyanobacteria. Thus, the aim of this research was to determine how variation in growth rate affected the physiology of marine Synechococcus WH8102 and CC9311 when growing under high N:P conditions. Experiments were carried out in chemostats with a media input N:P of 441 and we estimated the half saturation concentration for growth under P limiting conditions (K s,p) and cellular C:N:P ratios. The K s,p values were the lowest measured for any phytoplankton and on par with ambient P concentrations in oligotrophic regions. We also observed that both strains were able draw down P below 3 nM. Both K s,p and drawdown concentration were lower for the open ocean vs. coastal Synechococcus strain, which may be linked to differences in P acquisition genes in these strains. Cellular C:P and N:P ratios were significantly higher in relation to the Redfield ratio for both Synechococcus strains but we saw no difference in these ratios among growth rates or strains. These results demonstrate that Synechococcus can proliferate under very low P conditions and also that genetically different strains have unique physiological responses to P limitation.
    Frontiers in Microbiology 03/2015; 6. DOI:10.3389/fmicb.2015.00085 · 3.99 Impact Factor
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    • "e.g. Duplication of ferritin and Zn metallothionein genes Palenik et al. (2006), Zwirglmaier et al. (2008), Tai and Palenik (2009) Temperature/cold (Clade IV) Dominate in coastal and open ocean temperate and cold environments "
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    ABSTRACT: Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa.
    Marine Genomics 06/2014; 15. DOI:10.1016/j.margen.2014.03.002 · 1.79 Impact Factor
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    • "Clades of Prochlorococcus in the North Atlantic have more phosphorus-acquisition strategies than clades in the North Pacific, as an adaptation to chronic phosphate limitation (Coleman and Chisholm, 2010). Coastal clades of Synechococcus have higher number of regulatory systems and the use for metals than open ocean clades, the latter being adapted to relatively constant oligotrophic conditions (Palenik et al., 2006). To link ocean processes to microbial metabolism and to build better models for predicting responses to future ocean states (Azam and Malfatti, 2007), in light of this strain-level heterogeneity, new research tools are needed that assess individual and microbial community responses. "
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    ABSTRACT: Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.The ISME Journal advance online publication, 30 January 2014; doi:10.1038/ismej.2014.1.
    The ISME Journal 01/2014; 8(7). DOI:10.1038/ismej.2014.1 · 9.30 Impact Factor
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