Exploring the microbiome of the “star” freshwater diatom Asterionella formosa in a laboratory context

Abstract

Most of our knowledge on the mechanisms underlying diatom-bacterial interactions has been acquired through studies involving isolation of culturable partners. Here, we established a laboratory model of intermediate complexity between complex natural communities and laboratory pure culture models. We investigated the whole community formed by the freshwater diatom Asterionella formosa and its associated bacteria in a laboratory context, including both culturable and unculturable bacteria. Combining cellular and molecular approaches, we showed that in laboratory cultures, A. formosa microbiome was dynamic and comprised of numerous bacterial species (mainly Proteobacteria and Bacteroidetes). Using metagenomics, we explored several metabolic potentials present within the bacterial community. Our analyses suggested that bacteria were heterotrophic although a third of them (Alpha- and Beta-proteobacteria) could also be phototrophic. About 60% of the bacteria, phylogenetically diverse, could metabolize glycolate. The capacity to synthesize molecules such as B vitamins appeared unevenly distributed among bacteria. Altogether, our results brought insights into the bacterial diversity found in diatom-bacterial communities and hinted at metabolic interdependencies within the community that could result in diatom-bacterial and bacterial-bacterial interactions. The present work allowed us to explore the functional architecture of the bacterial community associated with A. formosa in culture and is complementary to field studies.

RNA Viruses in Aquatic Unicellular Eukaryotes

“…Asterionella is a genus of pennate diatoms identified as freshwater diatoms [102]. They are frequently found in star-shaped colonies (consisting up to 20 cells, but often eight) of individuals [103]. The species Asterionella glacialis was first reported from the Indian sector of the Antarctic Ocean.…”

Golden magic: RSH enzymes for (p)ppGpp metabolism in the diatom Phaeodactylum tricornutum

“…Genomic DNA from P. tricornutum Bohlin (strain number CCAP 1052/1A from Culture Collection of Algae and Protozoa, CCAP, Scottish Marine Institute) was isolated from cells grown in late-exponential phase, using an optimized method for diatoms (Puppo et al , 2017; Kojadinovic-Sirinelli et al , 2018). Sequences for the P. tricornutum RSH proteins: PtRSH1, PtRSH4a and PtRSH4b (accession codes: 11099, 7629 and 3397, respectively) were retrieved from Joint Genome Initiative (JGI) database (https://genome.jgi.doe.gov/Phatr2/Phatr2.home.html).…”

The case for research integration, from genomics to remote sensing, to understand biodiversity change and functional dynamics in the world's lakes

“…In such a situation we might envisage that interdisciplinary working could fill these gaps in the causal chain. As an example, the influence of changing water chemistry on phytoplankton growth may be mediated by bacterial–algal mutualisms or parasitism (Cirri & Pohnert, 2019; Kojadinovic‐Sirinelli et al, 2018). In the absence of recent developments in molecular and ‘omics approaches, we would have very limited understanding of these influential dynamics that are beginning to change the way we view freshwater food webs (Cooper & Smith, 2015).…”