The Bacterial and Fungal Microbiota of Saccharina latissima (Laminariales, Phaeophyceae)

Abstract

The sugar kelp Saccharina latissima dominates many temperate coastal ecosystems, plays key ecological roles and presents important economic potential. However, its microbiota remains poorly investigated, although it could play an important role in algal fitness. In this study, we combined high throughput Illumina-based DNA sequencing and Fluorescence In Situ Hybridization to perform a culture-independent investigation of the S. latissima bacterial and fungal microbiota. Up to 600 bacterial and 100 fungal Amplicon Sequence Variants were identified per algal individual, revealing diverse bacterial and fungal communities associated to S. latissima. Overall, bacterial communities were dominated by Proteobacteria, Actinobacteria, and Bacteroidetes, in particular Hyphomonadaceae and Cyclobacteriaceae. Fungal communities were dominated by Ascomycota and Basidiomycota, in particular Mycosphaerellaceae, Psathyrellaceae, and Bulleribasidiaceae. Our results also revealed a variable distribution of S. latissima microbiota, as two adjacent tissue samples typically contained distinct fungal and bacterial assemblages, and CARD-FISH analysis detected microbial endosymbionts (with a few epibionts). Complementary analyses showed that despite achieving a good sequencing coverage for each tissue sample, the unexpected diversity and variability of ASVs made the definition of a core fungal and bacterial microbiota difficult, and highlights novel avenues to overcome the limitations of current surface-sterilization and metabarcoding protocols.

Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes

“…To study the microbiota of natural populations, especially in remote regions, we need simple sampling protocols and storage methods. Methods available involve flash-freezing in liquid nitrogen (Tourneroche et al, 2020;van der Meer and Simpson, 1984), ethanol (Hammer et al, 2015;Song et al, 2016), various preserving reagents (Hammer et al, 2015;Song et al, 2016), and silica gel (Esteban et al, 2009;Hoarau et al, 2007;Phillips et al, 2001;Toishi, 1959). These methods can be applied to both algal tissue and surface swabs (Lachnit et al, 2011;Parrot et al, 2019;Qiu et al, 2019).…”

“…The sugar kelp or sea belt Saccharina latissima (L.) (Phaeophyceae, Laminariales) is one of the dominant kelp-forming species of brown macroalgae in Europe and is becoming a research model for holobiont studies and others (Staufenberger et al, 2008;Tourneroche et al, 2020;Wiese et al, 2009).…”

The Saccharina latissima microbiome: algal tissue matters more than region, season, and physiology

“…Notably, Staufenberger et al (2008) analysed the bacterial composition of Saccharina from two locations and seasons (Baltic and North Sea; January and April 2006) using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Later, Tourneroche et al (2020) used 16S metabarcoding and FISH to decipher the bacterial microbiota of young tissues of S. latissima sampled in Scotland on one date.…”

“…We found a higher proportion of Planctomycetes at the apex and Actinobacteriota almost exclusively in the meristem. Both phyla are classically found in brown macroalgae (Hollants et al, 2013) and on S. latissima [apex: (Staufenberger et al, 2008); meristem: (Tourneroche et al, 2020)]. Planctomycetes contain many sulfatase genes (Wegner et al, 2013), which help degrade sulphated polysaccharides.…”

Kelimpahan Fungi Kelas Dothideomycetes Pada Lumba-lumba Hidung Botol (Tursiops aduncus)

“…Komunitas fungi umumnya didominasi oleh filum Ascomycota dan Basidiomycota (Tourneroche et al, 2020;Wan et al, 2018). Berdasarkan hasil ITS metagenom ditemukan filum Ascomycota memiliki kelimpahan yang sangat tinggi mencapai 94% dari seluruh fungi yang ditemukan.…”