Aldehyde perception induces specific molecular responses in Laminaria digitata and affects algal consumption by a specialist grazer.

In the marine environment, distance signaling based on water-borne cues occurs during interactions between macroalgae and herbivores. In the brown alga Laminaria digitata from North-Atlantic Brittany, oligoalginates elicitation or grazing was shown to induce chemical and transcriptomic regulations, as well as emission of a wide range of volatile aldehydes, but their biological roles as potential defense or warning signals in response to herbivores remain unknown. In this context, bioassays using the limpet Patella pellucida and L. digitata were carried out for determining the effects of algal transient incubation with 4-hydroxyhexenal (4-HHE), 4-hydroxynonenal (4-HNE) and dodecadienal on algal consumption by grazers. Simultaneously, we have developed metabolomic and transcriptomic approaches to study algal molecular responses after treatments of L. digitata with these chemical compounds. The results indicated that, unlike the treatment of the plantlets with 4-HNE or dodecadienal, treatment with 4-HHE decreases algal consumption by herbivores at 100 ng.ml-1 . Moreover, we showed that algal metabolome was significantly modified according to the type of aldehydes, and more specifically the metabolite pathways linked to fatty acid degradation. RNAseq analysis further showed that 4-HHE at 100 ng.ml-1 can activate the regulation of genes related to oxylipin signaling pathways and specific responses, compared to oligoalginates elicitation. As kelp beds constitute complex ecosystems consisting of habitat and food source for marine herbivores, the algal perception of specific aldehydes leading to targeted molecular regulations could have an important biological role on kelps/grazers interactions.

Physiological effects of micro-plastics on the red algae, Grateloupia turuturu and Chondrus sp.

Plastics are the most abundant marine litter in the world's oceans and can be degraded into micro-plastics. These emerging pollutants negatively affect marine organisms, but little is known on the effects on macroalgae. In this study, we investigated the effects of micro-plastics on two species of red algae: Grateloupia turuturu and Chondrus sp. Grateloupia turuturu has a slippery surface while Chondrus sp. has a rough surface. Different surface characteristics of these macroalgae may affect adherence of micro-plastics. Both species were exposed to 5 different concentrations (0, 20, 200, 2000 and 20,000 ng/L) of polystyrene microspheres. Adherence capacity, accumulating micro-plastics on the surface was higher for Chondrus sp. than G. turuturu. Chondrus sp. at 20,000 ng/L only showed a decrease in growth rate and photosynthesis activity, and an increase of reactive oxygen species (ROS). However, G. turuturu was not significantly affected by micro-plastics at all tested concentrations. Shaded light and inhibition of gas flow by adhered micro-plastics may be a reason for the reduction of growth and photosynthesis and production of ROS. Based on this result, the toxic effects of micro-plastics appear to be species specific, dependent on the adherence capacity of macroalgae.

Temperature and high nutrients enhance hypo-salinity tolerance of the bloom forming green alga, Ulva prolifera.

The response of seaweeds to environmental stressors can be population-specific, and be related to the regime of their habitats. To explore the growth and physiological responses of Ulva prolifera, two strains of this alga (Korean and Chinese strains) were studied under an interaction of temperature (20 and 25 °C), nutrients (low nutrients: 50 µM of nitrate and 5 µM of phosphate; high nutrients: 500 µM of nitrate and 50 µM of phosphate) and salinity (20, 30 and 40 psu). The lowest growth rates of both strains were observed at 40 psu of salinity, independent of temperature and nutrient levels. At 20 °C and low nutrients condition, the carbon: nitrogen (C: N) ratio and growth rate in the Chinese strain were increased by 31.1% and 21.1% at a salinity of 20 psu in comparison to the salinity of 30 psu, respectively. High nutrients decreased the ratio of C:N in both strains with increasing tissue N content. At the same time, high nutrients also increased soluble protein and pigments contents, as well as photosynthetic and growth rates in both strains at the same salinity levels at 20 °C. Under 20 °C and high nutrients conditions, the growth rates and C:N ratio of both strains were significantly decreased with increasing salinity. The pigment, soluble protein and tissue N showed an inverse trend with the growth rate at all conditions. Moreover, the higher temperature of 25 °C inhibited the growth in both strains regardless of nutrients levels. The temperature of 25 °C enhanced the contents of tissue N and pigments in the Chinese strain only at the low nutrients level. The interaction of high nutrients and 25 °C led to the accumulation of tissue N and pigment contents in both strains under all salinity conditions compared to the 20 °C and high nutrients level. The temperature of 25 °C and high nutrients decreased the growth rate in the Chinese strain at both salinities of 30 and 40 psu more than the 20 °C, and low nutrients level at the same salinity. These results suggest that the Ulva blooms caused by the Chinese strain were more impacted at hypo-salinity levels compared to the Korean strain. Eutrophic or high nutrients level enhanced the salinity tolerance in both strains of U. prolifera. There will be a decline of U. prolifera blooms of the Chinese strain at hyper-salinity levels.

Exon shuffling potentiates a diverse repertoire of brown algal NB-ARC-TPR candidate immune receptor proteins via alternative splicing.

Like other organisms, brown algae are subject to diseases caused by bacteria, fungi, and viruses. Brown algal immunity mechanisms are not well characterized; however, there is evidence suggesting that pathogen receptors exist in brown algae. One key protein family likely associated with brown algal innate immunity possesses an NB-ARC domain analogous to innate immune proteins in plants and animals. In this study, we conducted an extensive survey of NB-ARC genes in brown algae and obtained insights into the domain organization and evolutionary history of the encoded proteins. Our data show that brown algae possess an ancient NB-ARC-tetratricopeptide repeat (NB-TPR) domain architecture. We identified an N-terminal effector domain, the four-helix bundle, which was not previously found associated with NB-ARC domains. The phylogenetic tree including NB-ARC domains from all kingdoms of life suggests the three clades of brown algal NB-TPRs are likely monophyletic, whereas their TPRs seem to have distinct origins. One group of TPRs exhibit intense exon shuffling, with various alternative splicing and diversifying selection acting on them, suggesting exon shuffling is an important mechanism for evolving ligand-binding specificities. The reconciliation of gene duplication and loss events of the NB-ARC genes reveals that more independent gene gains than losses have occurred during brown algal evolution, and that tandem duplication has played a major role in the expansion of NB-ARC genes. Our results substantially enhance our understanding of the evolutionary history and exon shuffling mechanisms of the candidate innate immune repertoire of brown algae.

Comparative Transcriptome Analysis Provides Insights into Response of Ulva compressa to Fluctuating Salinity Conditions.

Ulva compressa, a green tide-forming species, can adapt to hypo-salinity conditions, such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo-salinity stress tolerance, transcriptome-wide gene expression profiles in U. compressa were created using digital gene expression profiles. The RNA-seq data were analyzed based on the comparison of differently expressed genes involved in specific pathways under hypo-salinity and recovery conditions. The up-regulation of genes in photosynthesis and glycolysis pathways may contribute to the recovery of photosynthesis and energy metabolism, which could provide sufficient energy for the tolerance under long-term hyposaline stress. Multiple strategies, such as ion transportation and osmolytes metabolism, were performed to maintain the osmotic homeostasis. Additionally, several long noncoding RNA were differently expressed during the stress, which could play important roles in the osmotolerance. Our work will serve as an essential foundation for the understanding of the tolerance mechanism of U. compressa under the fluctuating salinity conditions.

HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching.

Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level. AVAILABILITY AND IMPLEMENTATION: HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git, and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks. CONTACT: yxmao@ouc.edu.cn or fenghen360@126.com.

Integrating transcriptomics and metabolomics to characterize the regulation of EPA biosynthesis in response to cold stress in seaweed Bangia fuscopurpurea.

Bangia fuscopurpurea is a traditional mariculture crop having high nutritional value, eicosapntemacnioc acid (EPA) production, and protein content. As an intertidal species, it can tolerate drastic changes in abiotic factors such as temperature, hydration, and light radiation; however, genomic information on the evolutionary aspect and mechanism of EPA enrichment in B. fuscopurpurea and the role of EPA in cold tolerance in this species remain elusive. We conducted transcriptome profile analysis in B. fuscopurpurea to investigate the biological functions of genes associated with resistance to various environment factors. We identified 41,935 unigenes that were assembled and applied to public databases to define their functional annotation (NR, GO, KEGG, KOG, and SwissProt). We further identified genes that encoded key enzymes in EPA biosynthesis; five paralogous genes encoding delta5 desaturase were detected in B. fuscopurpurea. Fatty acid profiling and gene expression analysis of B. fuscopurpurea grown under cold stress were simultaneously performed. The EPA content was increased by 29.8% in the samples grown at 4°C, while the total amount of fatty acids remained unchanged. Moreover, all the EPA biosynthesis-related desaturase and elongase genes were upregulated under cold stress. Thus, we hypothesized that diverse EPA biosynthesis pathways and significant increase in gene copy numbers of fatty acid desaturases, together with the concomitant elevation in the transcriptional level of genes associated with fatty acid metabolism, lead to EPA accumulation and subsequently affect membrane fluidity, contributing to cold stress resistance in B. fuscopurpurea. Our findings not only provide a fundamental genetic background for further research in B. fuscopurpurea, but also have important implications for screening and genetic engineering of algae and plants for EPA production.