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Ferris, MJ, Palenik B.  1998.  Niche adaptation in ocean cyanobacteria. Nature. 396:226-228.   10.1038/24297   AbstractWebsite

Small unicellular cyanobacteria (Synechococcus and Prochlorococcus ) are the most abundant photosynthetic microorganisms in the world's oceans, yet we know little of the genetic structure of these populations. Here we show that distinct clades of Prochlorococcus, and possibly of Synechococcus, are adapted to their specific surface and deep oceanic niches.

Foflonker, F, Price DC, Qiu H, Palenik B, Wang SY, Bhattacharya D.  2015.  Genome of the halotolerant green alga Picochlorum sp reveals strategies for thriving under fluctuating environmental conditions. Environmental Microbiology. 17:412-426.   10.1111/1462-2920.12541   AbstractWebsite

An expected outcome of climate change is intensification of the global water cycle, which magnifies surface water fluxes, and consequently alters salinity patterns. It is therefore important to understand the adaptations and limits of microalgae to survive changing salinities. To this end, we sequenced the 13.5Mbp genome of the halotolerant green alga PicochlorumSENEW3 (SE3) that was isolated from a brackish water pond subject to large seasonal salinity fluctuations. PicochlorumSE3 encodes 7367 genes, making it one of the smallest and most gene dense eukaryotic genomes known. Comparison with the pico-prasinophyte Ostreococcus tauri, a species with a limited range of salt tolerance, reveals the enrichment of transporters putatively involved in the salt stress response in PicochlorumSE3. Analysis of cultures and the protein complement highlight the metabolic flexibility of PicochlorumSE3 that encodes genes involved in urea metabolism, acetate assimilation and fermentation, acetoin production and glucose uptake, many of which form functional gene clusters. Twenty-four cases of horizontal gene transfer from bacterial sources were found in PicochlorumSE3 with these genes involved in stress adaptation including osmolyte production and growth promotion. Our results identify PicochlorumSE3 as a model for understanding microalgal adaptation to stressful, fluctuating environments.

Foflonker, F, Ananyev G, Qiu H, Morrison A, Palenik B, Dismukes GC, Bhattacharya D.  2016.  The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum. Algal Research-Biomass Biofuels and Bioproducts. 16:465-472.   10.1016/j.algal.2016.04.003   AbstractWebsite

The broadly halotolerant green alga, Picochlorum strain SENEW3, has a highly reduced nuclear genome of 13.5 Mbp that encodes only 7367 genes. It was isolated from a shallow, mesophilic brackish-water lagoon that experiences extreme changes in temperature, light, and in particular, salinity (freshwater to 3-fold seawater). We challenged Picochlorum cells with high or low salinity shock and used transcriptomic and chlorophyll fluorescence analyses to elucidate tolerance to salinity fluctuation. The transcriptome analysis showed that one-half of the coding regions are differentially expressed in response to salinity changes. In addition, a significant number of co-expressed genes (usually from different metabolic pathways) are co-localized in the genome, forming 2-10 gene clusters. Whereas the overall salt stress response in Picochlorum SENEW3 is similar to that in other salt-tolerant algae, the "operon-like" structure in this species likely contributes to rapid recovery during salinity fluctuation. In summary, our work elucidates how evolutionary forces play out in a streamlined genome. Picochlorum SENEW3 relies on a broad array of adaptations from the reliance on horizontally transferred adaptive genes to the co-localization of stress response genes and a robust photosystem II to deal with a fluctuating environment. These attributes make Picochlorum SENEW3 of great biotechnological interest. (C) 2016 Elsevier B.V. All rights reserved.