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Title: The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing
Author: Keeling, Burki, Wilcox, Allam, Allen, Amaral-Zettler, Armbrust, Archibald, Bharti, Bell, Beszteri, Bidle, Cameron, Campbell, Caron, Cattolico, Collier, Coyne, Davy, Deschamps, Dyhrman, Edvardsen, Gates, Gobler, Greenwood, Guida, Jacobi, Jakobsen, James, Jenkins, John, Johnson, Juhl, Kamp, Katz, Kiene, Kudryavtsev, Leander, Lin, Lovejoy, Lynn, Marchetti, McManus, Nedelcu, Menden-Deuer, Miceli, Mock, Montresor, Moran, Murray, Nadathur, Nagai, Ngam, Palenik, Pawlowski, Petroni, Piganeau, Posewitz, Rengefors, Romano, Rumpho, Rynearson, Schilling, Schroeder, Simpson, Slamovits, Smith, Smith, Smith, Sosik, Stief, Theriot, Twary, Umale, Vaulot, Wawrik, Wheeler, Wilson, Xu, Zingone, Worden
Date: 2014-01-01T00:00:00Z

Title: The evolution of silicon transporters in diatoms
Description: Diatoms are highly productive single-celled algae that form an intricately patterned silica cell wall after every cell division. They take up and utilize silicic acid from seawater via silicon transporter (SIT) proteins. This study examined the evolution of the SIT gene family to identify potential genetic adaptations that enable diatoms to thrive in the modern ocean. By searching for sequence homologs in available databases, the diversity of organisms found to encode SITs increased substantially and included all major diatom lineages and other algal protists. A bacterial-encoded gene with homology to SIT sequences was also identified, suggesting that a lateral gene transfer event occurred between bacterial and protist lineages. In diatoms, the SIT genes diverged and diversified to produce five distinct clades. The most basal SIT clades were widely distributed across diatom lineages, while the more derived clades were lineage-specific, which together produced a distinct repertoire of SIT types among major diatom lineages. Differences in the predicted protein functional domains encoded among SIT clades suggest that the divergence of clades resulted in functional diversification among SITs. Both laboratory cultures and natural communities changed transcription of each SIT clade in response to experimental or environmental growth conditions, with distinct transcriptional patterns observed among clades. Together, these data suggest that the diversification of SITs within diatoms led to specialized adaptations among diatoms lineages, and perhaps their dominant ability to take up silicic acid from seawater in diverse environmental conditions.
Author: Durkin, Koester, Bender, Armbrust

Title: Frustule-related gene transcription and the influence of diatom community composition on silica precipitation in an iron-limited environment
Description: A microcosm study in iron-limited waters of the northeast subarctic Pacific Ocean was conducted to examine how iron availability affects the frustule-related response of individual diatoms and thus the total quantity of silica precipitated by the community. New silica precipitated per cell was estimated using the fluorescent cell stain 2-(4-pyridyl)-5{[4-dimethylaminoethyl-aminocarbamoyl)-methoxy]phenyl}oxazole (PDMPO). Differences in new silica precipitation within a particular genus before and after iron enrichment were small compared to differences among genera, indicating that the quantity of total silica precipitated is particularly sensitive to community composition. Transcriptional patterns of genes encoding silicon transporters, aminopropyltransferases, chitin synthases, and a protein with uncharacterized function were measured in natural populations to identify indicators of the frustule-related responses of different genera to iron limitation. Transcripts associated with silicon transporters were the most readily detectable in three metatranscriptome datasets and were capable of resolving species composition shifts and physiological responses. Silicon transporter transcripts from a distinct phylogenetic clade were most abundant in the iron-limited community, and transcripts from a separate clade were more abundant in the community that bloomed after iron enrichment. Transcripts of the gene present in the ironlimited community were also more abundant in iron-limited laboratory cultures of Pseudo-nitzschia multiseries, suggesting that this gene plays a role in silicon uptake during iron limitation. The responses of individual cells, as detected in this study, determine how the community influences silicon cycling in iron-limited environments., published
Author: Durkin, Marchetti, Bender, Truong, Morales, Mock, Armbrust

Title: Chitin in Diatoms and Its Association with the Cell Wall
Description: Chitin is a globally abundant polymer widely distributed throughout eukaryotes that has been well characterized in only a few lineages. Diatoms are members of the eukaryotic lineage of stramenopiles. Of the hundreds of diatom genera, two produce long fibers of chitin that extrude through their cell walls of silica. We identify and describe here genes encoding putative chitin synthases in a variety of additional diatom genera, indicating that the ability to produce chitin is more widespread and likely plays a more central role in diatom biology than previously considered. Diatom chitin synthases fall into four phylogenetic clades. Protein domain predictions and differential gene expression patterns provide evidence that chitin synthases have multiple functions within a diatom cell. Thalassiosira pseudonana possesses six genes encoding three types of chitin synthases. Transcript abundance of the gene encoding one of these chitin synthase types increases when cells resume division after short-term silicic acid starvation and during short-term limitation by silicic acid or iron, two nutrient conditions connected in the environment and known to affect the cell wall. During long-term silicic acid starvation transcript abundance of this gene and one additional chitin synthase gene increased at the same time a chitin-binding lectin localized to the girdle band region of the cell wall. Together, these results suggest that the ability to produce chitin is more widespread in diatoms than previously thought and that a subset of the chitin produced by diatoms is associated with the cell wall., published
Author: Durkin, Mock, Armbrust