Three Novel Bacteria Associated with Two Centric Diatom Species from the Mediterranean Sea, Thalassiosira rotula and Skeletonema marinoi.

Federica Di Costanzo,Adele Cutignano,Francesco Esposito,Giovanna Romano,Marla Trindade,Leonardo Joaquim Van Zyl,Valeria Di Dato

doi:10.3390/ijms222413199

Abstract

Diatoms are a successful group of microalgae at the base of the marine food web. For hundreds of millions of years, they have shared common habitats with bacteria, which favored the onset of interactions at different levels, potentially driving the synthesis of biologically active molecules. To unveil their presence, we sequenced the genomes of bacteria associated with the centric diatom Thalassiosira rotula from the Gulf of Naples. Annotation of the metagenome and its analysis allowed the reconstruction of three bacterial genomes that belong to currently undescribed species. Their investigation showed the existence of novel gene clusters coding for new polyketide molecules, antibiotics, antibiotic-resistance genes and an ectoine production pathway. Real-time PCR was used to investigate the association of these bacteria with three different diatom clones and revealed their preference for T. rotula FE80 and Skeletonema marinoi FE7, but not S. marinoi FE60 from the North Adriatic Sea. Additionally, we demonstrate that although all three bacteria could be detected in the culture supernatant (free-living), their number is up to 45 times higher in the cell associated fraction, suggesting a close association between these bacteria and their host. We demonstrate that axenic cultures of T. rotula are unable to grow in medium with low salinity (<28 ppt NaCl) whereas xenic cultures can tolerate up to 40 ppt NaCl with concomitant ectoine production, likely by the associated bacteria.

Highlights

Since diatoms are at the base of the marine food web, they are fundamental to the health of the planet, playing a crucial role in carbon fixation [7] and contribute to the formation of oil deposits sinking to the bottom of the oceans due to their heavy frustule [8]
Within this work, based on metagenome analysis of bacteria associated with T. rotula we identified three new bacterial species, named Clusters 1, 2 and 8 (Cl-1, Cl-2, Cl-8)
We identified three new bacterial species associated to at least two diatom species, i.e., Skeletonema marinoi and Thalassiosira rotula

Summary

Introduction

Since diatoms are at the base of the marine food web, they are fundamental to the health of the planet, playing a crucial role in carbon fixation [7] and contribute to the formation of oil deposits sinking to the bottom of the oceans due to their heavy frustule [8]. They are represented by more than 200,000 different species able to adapt to every marine niche and bloom in both coastal and oceanic areas, or wherever sufficient nutrients can sustain their growth [8,9]. Bacteria seem to establish a stable long-term association with diatoms [14], and certain bacterial orders, in particular Rhizobiales and Rhodobacterales, tend to co-occur with Symbiodiniaceae dinoflagellates when establishing symbiosis with other organisms [18]

Methods

Discussion

Conclusion