A highly prevalent filamentous algal endophyte in natural populations of the sugar kelp Saccharina latissima is not detected during cultivation in Northern Brittany

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Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)

<p/> <p>Background</p> <p>Brown algae of the genus <it>Ectocarpus </it>exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of <it>E. siliculosus </it>as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus <it>Ectocarpus </it>both at the genome and the transcriptome level.</p> <p>Results</p> <p>We used an <it>E. siliculosus </it>gene expression microarray based on EST sequences from the genome-sequenced strain (reference strain) to carry out comparative genome hybridizations for five <it>Ectocarpus </it>strains: four <it>E. siliculosus </it>isolates (the male genome strain, a female strain used for outcrosses with the genome strain, a strain isolated from freshwater, and a highly copper-tolerant strain), as well as one strain of the sister species <it>E. fasciculatus</it>. Our results revealed significant genomic differences between ecotypes of the same species, and enable the selection of conserved probes for future microarray experiments with these strains. In the two closely related strains (a male and a female strain used for crosses), genomic differences were also detected, but concentrated in two smaller genomic regions, one of which corresponds to a viral insertion site.</p> <p>Conclusion</p> <p>The high variability between strains supports the concept of <it>E. siliculosus </it>as a complex of cryptic species. Moreover, our data suggest that several parts of the <it>Ectocarpus </it>genome may have evolved at different rates: high variability was detected particularly in transposable elements and fucoxanthin chlorophyll a/c binding proteins.</p

Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus

<p>Abstract</p> <p>Background</p> <p>Brown algae are plant multi-cellular organisms occupying most of the world coasts and are essential actors in the constitution of ecological niches at the shoreline. <it>Ectocarpus siliculosus </it>is an emerging model for brown algal research. Its genome has been sequenced, and several tools are being developed to perform analyses at different levels of cell organization, including transcriptomic expression analyses. Several topics, including physiological responses to osmotic stress and to exposure to contaminants and solvents are being studied in order to better understand the adaptive capacity of brown algae to pollution and environmental changes. A series of genes that can be used to normalise expression analyses is required for these studies.</p> <p>Results</p> <p>We monitored the expression of 13 genes under 21 different culture conditions. These included genes encoding proteins and factors involved in protein translation (ribosomal protein 26S, EF1alpha, IF2A, IF4E) and protein degradation (ubiquitin, ubiquitin conjugating enzyme) or folding (cyclophilin), and proteins involved in both the structure of the cytoskeleton (tubulin alpha, actin, actin-related proteins) and its trafficking function (dynein), as well as a protein implicated in carbon metabolism (glucose 6-phosphate dehydrogenase). The stability of their expression level was assessed using the Ct range, and by applying both the geNorm and the Normfinder principles of calculation.</p> <p>Conclusion</p> <p>Comparisons of the data obtained with the three methods of calculation indicated that EF1alpha (EF1a) was the best reference gene for normalisation. The normalisation factor should be calculated with at least two genes, alpha tubulin, ubiquitin-conjugating enzyme or actin-related proteins being good partners of EF1a. Our results exclude actin as a good normalisation gene, and, in this, are in agreement with previous studies in other organisms.</p

A highly prevalent filamentous algal endophyte in natural populations of the sugar kelp Saccharina latissima is not detected during cultivation in Northern Brittany

The sugar kelp Saccharina latissima is cultivated in Europe for food, feed and ultimately the production of chemical commodities and bioenergy. Being cultivated in the open sea, S. latissima is exposed to potentially harmful organisms, such as Laminarionema elsbetiae, a filamentous brown algal endophyte with a very high prevalence in wild populations of European S. latissima. As it was shown previously that S. latissima sporophytes get infected by L. elsbetiae very early in their life, seeding the spores on collectors and keeping them under controlled conditions during the critical time of a possible infection with filamentous endophytes could be advantageous over direct seeding techniques, where the ropes are deployed within days after seeding. We used a qPCR-assay to assess the prevalence of the endophyte L. elsbetiae in S. latissima cultivated during winter in Northern Brittany, comparing individuals from direct-seeded ropes and collector-seeded lines that were kept in laboratory conditions for different time spans. No DNA of the endophyte was detected in the samples, suggesting that either the kelps were not infected or the amount of endophytic filaments were below the detection rate of the qPCR assay. Furthermore, L. elsbetiae could not be detected in the seawater surrounding the kelp farm, indicating that L. elsbetiae is not fertile or disperses at a very small scale in Northern Brittany during the deployment time of young kelps. Our results suggest that infections of cultivated S. latissima with the endophyte L. elsbetiae might be a minor problem in kelp farms in Northern Brittany if the seeding production is kept under controlled conditions without external contamination

The Saccharina latissima microbiome: Effects of region, season, and physiology

IntroductionSaccharina latissima is a canopy-forming species of brown algae and, as such, is considered an ecosystem engineer. Several populations of this alga are exploited worldwide, and a decrease in the abundance of S. latissima at its southern distributional range limits has been observed. Despite its economic and ecological interest, only a few data are available on the composition of microbiota associated with S. latissima and its role in algal physiologyn.MethodsWe studied the whole bacterial community composition associated with S. latissima samples from three locations (Brittany, Helgoland, and Skagerrak) by 16S metabarcoding analyses at different scales: algal blade part, regions, season (at one site), and algal physiologic state.Results and DiscussionWe have shown that the difference in bacterial composition is driven by factors of decreasing importance: (i) the algal tissues (apex/meristem), (ii) the geographical area, (iii) the seasons (at the Roscoff site), and (iv) the algal host’s condition (healthy vs. symptoms). Overall, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia dominated the general bacterial communities. Almost all individuals hosted bacteria of the genus Granulosicoccus, accounting for 12% of the total sequences, and eight additional core genera were identified. Our results also highlight a microbial signature characteristic for algae in poor health independent of the disease symptoms. Thus, our study provides a comprehensive overview of the S. latissima microbiome, forming a basis for understanding holobiont functioning

An expressed sequence tag analysis of thallus and regenerating protoplasts of Chondrus crispus (Gigartinales, Rhodophyceae)

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Identification of stress gene transcripts in Laminaria digitata (Phaeophyceae) protoplast cultures by expressed sequence tag analysis

To characterize stress and defense-induced genes in the brown alga Laminaria digitata (Hudson) J.V. Lamouroux, 1985 expressed sequence tags (ESTs) were generated from L. digitata protoplasts. Comparison of the ESTs with public databases allowed putative functions to be assigned to 45% of the sequences. Comparison with ESTs from L. digitata sporophytes showed that protoplasts expressed more stress genes than intact thalli. Several transcripts in the stress gene class coded for proteins involved in cell protection against oxygen radicals, including thioredoxins (six ESTs), thioredoxin peroxidases (two ESTs), and glutathione-S-transferase (GST) (41 ESTs). The GSTs appear to be part of the sigma class, making them the first GST sigma identified in a photosynthetic organism. Other stress genes included a new type of vanadium-dependent bromoperoxidases (vBPO) showing 71% similarity with vBPOs previously identified in the sporophytic-thalli phase of L. digitata. The ESTs coding for 22 different mannuronan-C5-epimerases were identified among the cell wall biosynthesis genes, and several ESTs showed similarity with the genome of the Ectocarpus siliculosus virus

NormFinder analysis vs. geNorm analysis of the 14 housekeeping genes.

<p>The stability of expression of the 14 candidate genes was compared between the NormFinder method (abscissa axis) and the geNorm method (ordinate axis). (R² = 0.94).</p

NormFinder analysis of the expression stability of the 14 housekeeping genes.

<p>The stability of expression of the 14 candidate genes was calculated using the NormFinder method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086574#pone.0086574-Andersen1" target="_blank">[11]</a>. A. all samples, B. culture samples, C. field samples.</p