Annotated Genome Sequence of the High-Biomass-Producing Yellow-Green Alga Tribonema minus.

Here, we report the annotated genome sequence for a heterokont alga from the class Xanthophyceae. This high-biomass-producing strain, Tribonema minus UTEX B 3156, was isolated from a wastewater treatment plant in California. It is stable in outdoor raceway ponds and is a promising industrial feedstock for biofuels and bioproducts.

Characterization of a novel strain of Tribonema minus demonstrating high biomass productivity in outdoor raceway ponds.

Photosynthetic algae represent a large, diverse bioresource potential. Yellow-green algae of the genus Tribonema are candidates for production of biofuels and other bioproducts. We report on a filamentous isolate from an outdoor raceway polyculture growing on municipal reclaimed wastewater which we classified as T. minus. Over one year of cultivation in 3.5 m2 raceway ponds fed by reclaimed municipal wastewater, T. minus cultures were more productive than the native algal polycultures, with annual average productivities of 15.9 ± 0.3 and 13.4 ± 0.4 g/m2/day, respectively. The biochemical composition of T. minus biomass grown outdoors was constant year-round, with 28.3 ± 0.4% carbohydrates, 37.6 ± 0.7% proteins, and 6.1 ± 0.3% fatty acids (measured as methyl esters), with up to 4.0% of the valuable omega-3 eicosapentaenoic acid, on an ash-free dry-weight basis. In summary, T. minus was more productive, easier to harvest and produced higher quality biomass than the native polycultures.

Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production.

Microalgae are among the most diverse organisms on the planet, and as a result of symbioses and evolutionary selection, the configuration of core metabolic networks is highly varied across distinct algal classes. The differences in photosynthesis, carbon fixation and processing, carbon storage, and the compartmentation of cellular and metabolic processes are substantial and likely to transcend into the efficiency of various steps involved in biofuel molecule production. By highlighting these differences, we hope to provide a framework for comparative analyses to determine the efficiency of the different arrangements or processes. This sets the stage for optimization on the based on information derived from evolutionary selection to diverse algal classes and to synthetic systems.

A self-propagating system for Ge incorporation into nanostructured silica.

Technologically-relevant levels of Ge can be incorporated into cell wall silica of the diatom Thalassiosira pseudonana with no aberration in structure at low levels, whereas higher levels alter structure.

Characterization of a modular, cell-surface protein and identification of a new gene family in the diatom Thalassiosira pseudonana.

We report the characterization of a cell-surface protein isolated from copper-stressed cells of the centric diatom Thalassiosira pseudonana Hasle and Heimdal (CCMP 1335). This protein has an apparent molecular weight of 100kDa and is highly acidic. The 100kDa protein (p100) sequence is comprised almost entirely of a novel domain termed TpRCR for T. pseudonana repetitive cysteine-rich domain, that is repeated 8 times and that contains conserved aromatic, acidic, and potential metal-binding amino acids. The analysis of the T. pseudonana genome suggests that p100 belongs to a large family of modular proteins that consist of a variable number of TpRCR domain repeats. Based on cell surface biotinylation and antibody data, p100 appears to migrate more rapidly with SDS-PAGE when extracted from cells exposed to high levels of copper; however, the discovery of a large family of TpRCR domain-containing proteins leaves open the possibility that the antibody may be cross-reacting with members of this protein family that are responding differently to copper. The response of the gene encoding p100 at the mRNA level during synchronized progression through the normal cell cycle is similar to previously characterized genes in T. pseudonana encoding cell wall proteins called silaffins.

Gene expression induced by copper stress in the diatom Thalassiosira pseudonana.

Utilizing a PCR-based subtractive cDNA approach, we demonstrated that the marine diatom Thalassiosira pseudonana exhibits a rapid response at the gene level to elevated concentrations of copper and that this response attenuates over 24 h of continuous exposure. A total of 16 copper-induced genes were identified, 11 of which were completely novel; however, many of the predicted amino acid sequences had characteristics suggestive of roles in ameliorating copper toxicity. Most of the novel genes were not equivalently induced by H2O2- or Cd-induced stress, indicating specificity in response. Two genes that could be assigned functions based on homology were also induced under conditions of general cellular stress. Half of the identified genes were located within two inverted repeats in the genome, and novel genes in one inverted repeat had mRNA levels induced by approximately 500- to 2,000-fold by exposure to copper for 1 h. Additionally, some of the inverted repeat genes demonstrated a dose-dependent response to Cu, but not Cd, and appear to belong to a multigene family. This multigene family may be the diatom functional homolog of metallothioneins.

The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.