Exploring the Cultivable Ectocarpus Microbiome

Abstract

Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.

Metabolic Complementarity Between a Brown Alga and Associated Cultivable Bacteria Provide Indications of Beneficial Interactions

“…Ten bacterial strains were selected from the 46 isolated by KleinJan et al (2017) from Ectocarpus subulatus. They were grown in liquid Zobell and/or diluted R2A until bacterial growth was visible with the naked eye (∼3 days at room temperature), and their identity was confirmed by sequencing of the 16S rRNA gene with the primers 8F and 1492R (KleinJan et al, 2017).…”

“…Ten bacterial strains were selected from the 46 isolated by KleinJan et al (2017) from Ectocarpus subulatus. They were grown in liquid Zobell and/or diluted R2A until bacterial growth was visible with the naked eye (∼3 days at room temperature), and their identity was confirmed by sequencing of the 16S rRNA gene with the primers 8F and 1492R (KleinJan et al, 2017). Bacterial DNA was extracted using the UltraClean R Microbial DNA isolation kit (MoBio, Qiagen, Hilden, Germany) and used for standard pair-end sequencing at the GENOMER platform (FR2424, Station Biologique de Roscoff), using Illumina Miseq technology (V3 chemistry, 2 × 300 bp).…”

“…Here we have applied the MiSCoTo tool to the filamentous brown alga Ectocarpus siliculosus, a model filamentous brown alga with an available metabolic network (Prigent et al, 2014), as well as a selection of 10 Ectocarpus-derived bacteria (KleinJan et al, 2017). We then selected specific minimal microbial consortia for in vivo testing of the proposed hypotheses (growth rate, production of specific metabolites).…”

Revisiting australianectocarpus subulatus(phaeophyceae) from the hopkins river: distribution, abiotic environment, and associated microbiota

“…The E. subulatus strain from Hopkins River Falls has further been used for physiological experiments: it can grow in both seawater and fresh water and its transcriptomic and metabolic acclimation to these conditions has been examined (Dittami et al 2012) along with the composition of its cell wall with regard to sulfated polysaccharides (Torode et al 2015). Moreover, the capacity of the freshwater strain to grow in low salinities has been shown to depend on its associated microbial community (Dittami et al 2016), and extensive efforts have been made to develop a collection of cultivable bacteria to study this phenomenon (KleinJan et al 2017).…”

Revisiting Australian Ectocarpus subulatus (Phaeophyceae) From the Hopkins River: Distribution, Abiotic Environment, and Associated Microbiota

“…Extensive efforts have been made to develop a collection of cultivable bacteria to study this phenomenon (KleinJan et al. ).…”