Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea

Ulva: An emerging green seaweed model for systems biology

Green seaweeds exhibit a wide range of morphologies and occupy various ecological niches, spanning from freshwater to marine and terrestrial habitats. These organisms, which predominantly belong to the class Ulvophyceae, showcase a remarkable instance of parallel evolution toward complex multicellularity and macroscopic thalli in the Viridiplantae lineage. Within the green seaweeds, several Ulva species ("sea lettuce") are model organisms for studying carbon assimilation, interactions with bacteria, life cycle progression, and morphogenesis. Ulva species are also notorious for their fast growth and capacity to dominate nutrient-rich, anthropogenically disturbed coastal ecosystems during "green tide" blooms. From an economic perspective, Ulva has garnered increasing attention as a promising feedstock for the production of food, feed, and biobased products, also as a means of removing excess nutrients from the environment. We propose that Ulva is poised to further develop as a model in green seaweed research. In this perspective, we focus explicitly on Ulva mutabilis/compressa as a model species and highlight the molecular data and tools that are currently available or in development. We discuss several areas that will benefit from future research or where exciting new developments have been reported in other Ulva species.

From model organism to application: Bacteria-induced growth and development of the green seaweed Ulva and the potential of microbe leveraging in algal aquaculture

The marine green macroalga Ulva (Chlorophyta, Ulvales), also known as sea lettuce, coexists with a diverse microbiome. Many Ulva species proliferate in nature and form green algal blooms ("green tides"), which can occur when nutrient-rich wastewater from agricultural or densely populated areas is flushed into the sea. Bacteria are necessary for the adhesion of Ulva to its substrate, its growth, and the development of its blade morphology. In the absence of certain bacteria, Ulva mutabilis develops into a callus-like morphotype. However, with the addition of the necessary marine bacteria, the entire morphogenesis can be restored. Surprisingly, just two bacteria isolated from U. mutabilis are sufficient for inducing morphogenesis and establishing the reductionist system of a tripartite community. While one bacterial strain causes algal blade cell division, another causes the differentiation of basal cells into a rhizoid and supports cell wall formation because of a low concentration of the morphogen thallusin (below 10^-10 mol/L). This review focuses on the research conducted on this topic since 2015, discusses how U. mutabilis has developed into a model organism in chemical ecology, and explores the questions that have already been addressed and the perspectives that a reductionist model system allows. In particular, the field of systems biology will achieve a comprehensive, quantitative understanding of the dynamic interactions between Ulva and its associated bacteria to better predict the behavior of the system as a whole. The reductionist approach has enabled the study of the bacteria-induced morphogenesis of Ulva. Specific questions regarding the optimization of cultivation conditions as well as the yield of raw materials for the food and animal feed industries can be answered in the laboratory and through applied science. Genome sequencing, the improvement of genetic engineering tools, and the first promising attempts to leverage macroalgae-microbe interactions in aquaculture make this model organism, which has a comparatively short parthenogenetic life cycle, attractive for both fundamental and applied research. The reviewed research paves the way for the synthetic biology of macroalgae-associated microbiomes in sustainable aquacultures.

Complete organellar genomes of six Sargassum species and development of species-specific markers

Sargassum is one of the most important brown algal genera that can be used as food and raw material for medicinal purpose, and has various beneficial effects. As the classification of Sargassum species is currently based on their morphological characteristics, organellar genome sequences of Sargassum would provide important information for accurate identification of species and developing species-specific markers. We sequenced the complete organellar genomes of six Sargassum species, including the first complete chloroplast genome sequences of S. fulvellum, S. serratifolium, S. macrocarpum, and S. siliquastrum, and the first complete mitochondrial genome sequences of S. fulvellum, S. serratifolium, and S. macrocarpum. The chloroplast genomes of the 6 Sargassum species contained 139 protein-coding genes (PCGs), and the mitochondrial genomes possessed 37 PCGs. A comparative study was performed between the newly sequenced organellar genomes and 44 other species belonging to class Phaeophyceae. Phylogenetic relationships using PCGs shared by Phaeophyceae species were constructed with IQ-TREE 2 using the maximum likelihood method. In addition, we developed real-time PCR markers based on SNPs to distinguish the 6 Sargassum species. Our results provide useful information for establishing phylogenetic relationships between brown algae.