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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., (© 2016 The Authors. Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America.)

Diatoms are photoautotrophic organisms capable of growing on a variety of inorganic and organic nitrogen sources. Discovery of a complete urea cycle in diatoms was surprising, as this pathway commonly functions in heterotrophic organisms to rid cells of waste nitrogen. To determine how the urea cycle is integrated into cellular nitrogen metabolism and energy management, the centric diatom Thalassiosira pseudonana was maintained in semi-continuous batch cultures on nitrate, ammonium, or urea as the sole nitrogen source, under a 16: 8 light: dark cycle and at light intensities that were low, saturating, or high for growth. Steady-state transcript levels were determined for genes encoding enzymes linked to the urea cycle, urea hydrolysis, glutamine synthesis, pyrimidine synthesis, photorespiration, and energy storage. Transcript abundances were significantly affected by nitrogen source, light intensity and a diel cycle. The impact of N source on differential transcript accumulation was most apparent under the highest light intensity. Models of cellular metabolism under high light were developed based on changes in transcript abundance and predicted enzyme localizations. We hypothesize that the urea cycle is integrated into nitrogen metabolism through its connection to glutamine and in the eventual production of urea. These findings have important implications for nitrogen flow in the cell over diel cycles at surface ocean irradiances., (Copyright © 2011 Elsevier GmbH. All rights reserved.)

In the modern ocean, phytoplankton maintain extremely high primary production/biomass ratios, indicating that they bloom, die, and are replaced weekly. The molecular mechanisms regulating cellular mortality and turnover are largely unknown, even though they effectively short-circuit carbon export to the deep ocean and channel primary productivity to microbial food webs. Here, we present morphological, biochemical, and molecular evidence of caspase-mediated, autocatalytic programmed cell death (PCD) in the diatom Thalassiosira pseudonana in response to iron starvation. Transmission electron microscopy revealed internal degradation of nuclear, chloroplastic, and mitochondrial organelles, all while the plasma membranes remained intact. Cellular degradation was concomitant with dramatic decreases in photosynthetic efficiency, externalization of phosphatidylserine, and significantly elevated caspase-specific activity, with the addition of a broad-spectrum caspase inhibitor rescuing cells from death. A search of the T. pseudonana genome identified six distinct putative metacaspases containing a conserved caspase domain structure. Quantitative reverse transcription-PCR and Western blot analysis revealed differential gene and protein expression of T. pseudonana metacaspases, some of which correlated with physiological stress and caspase activity. Taken together with the recent discovery of the metacaspase-mediated viral infection of phytoplankton (K. D. Bidle, L. Haramaty, J. Barcelos-Ramos, and P. G. Falkowski, Proc. Natl. Acad. Sci. USA 104:6049-6054, 2007), our findings reveal a key role for metacaspases in the turnover of phytoplankton biomass in the oceans. Furthermore, given that Fe is required for photosynthetic electron transfer and is chronically limiting in a variety of oceanic systems, including high-nutrient low-chlorophyll regions, our findings provide a potential ecological context for PCD in these unicellular photoautotrophs.

Microcosm experiments were conducted along the Washington and Oregon coasts in May 2009, May 2010, and July 2010 to determine whether variation in the supply of silicic acid from the Columbia River could influence the silicification and sinking potential of coastal diatom blooms. The chlorophyll a concentration increased similarly in communities incubated with added nitrate or both nitrate and silicic acid, indicating that growth was limited by nitrate availability. Communities that grew in the treatment with added silicic acid and nitrate were more silicified than communities in the treatment with only nitrate added. No difference in community composition was detected between these treatments in three out of four experiments. Isolates of Minutocellus, Cylindrotheca, Thalassiosira, and Odontella were obtained from the microcosm experiment conducted in May 2010 and were maintained in the laboratory in 20 µmol L-1 silicic acid. All four diatom isolates contained ~ 2.5 times more silica per cell when silicic acid concentration in the media was increased to 80 µmol L-1 . The intensity of a fluorescent cellular stain of newly precipitated silica (2-(4-pyridyl)-5{[4-dimethylaminoethyl-aminocarbamoyl)-methoxy]phenyl}oxazole) strongly correlated with silica content among species, but was a less sensitive indicator of changing silicification within a single species. Changes in silicification were not correlated with changes in the transcript abundance of silicic acid transporters. Sinking rates increased roughly 2-fold for cells that contained ~ 2.5 times more silica. Variation in silicic acid supply alters the silicification of nitrate-fueled coastal diatom blooms and the potential sink of carbon from coastal zones. [ABSTRACT FROM AUTHOR]